Baker, Brett

Brett J Baker

Assistant Professor
Department of Marine Science

Office Location
MSI 219

Postal Address
The University of Texas at Austin
Mar Sci Inst-Port Aran
750 Channel View Dr
Port Aransas, TX 78373

Ph.D., Earth and Environmental Sciences, University of Michigan, 2014

MS, Department of Biological Sciences, University of Wisconsin-Milwaukee, 2000

B.S., Biological Sciences, University of Wisconsin-Milwaukee, 1997


Microorganisms are key mediators in nearly all of the planet’s elemental cycles. However, our understanding of the ecological roles of many groups of microbes has been hampered by low-resolution analytical approaches to studying the staggering diversity present in nature. As a result the tree of life is full of branches, which remain undiscovered, and those, which have only been identified in single-gene sequencing surveys (Baker and Dick, 2013). This is a fundamental gap in our understanding of biology. Filling in the genomic gaps in the tree of life will provide a rich context to understand the evolution of life on the planet and will provide us with a genetic understanding of how microbial communities drive biogeochemical cycles.

Recent advances in DNA sequencing technologies and computational analyses have made it possible to reconstruct the genomes and transcriptomes of uncultured natural populations (Baker et al. 2010, 2012 and 2013). I have been involved in the development (Dick et al. 2009) and implementation of environmental omics since the beginning. I was involved in the first metaproteomic study of a microbial community (Ram et al. 2005) and have been using these approaches to track fine-scale evolutionary processes (Denef et al. 2010). Using these techniques I discovered deeply branching, novel groups of microbes (Archaea referred to as ARMAN) that are close to the predicted lower size limit of an organism (Baker et al. 2006). Obtaining complete genomes of the ARMAN phylum revealed that they have signatures of inter-species interactions and form connections to other species in nature (Baker et al. 2010).

More recently, my laboratory has reconstructed the genomes of hundreds of widespread, uncultured sediment microbes to understand how ecological roles are partitioned in these microbial communities. Many of the genomes belong to phyla which have no previous genomic representation and discovered three new groups of bacteria they play important roles in the global carbon cycle (Baker et al. 2015; Lazar, et al, Environ Micro). One of the new branches for which we have obtained several genomes for is a deeply branched member (Thorarchaeota) (Seitz et al. 2016). These genomes have provided rich insights into the evolutionary histories of life on the planet and we have been able to map the flow of carbon and energy, a microbial food web, through sediments with unprecedented detail (Baker et al. 2015).


Bowers RM, Kyrpides N, Stepanauskas R, Harmon-Smith M, Doud D, Jarett J, Schulz F, Reddy TBK, Rivers A, Eloe-Fadrosh E, Tringe S, Ivanova N, Copeland A, Clum A, Becraft E, Malmstrom R, Birren B, Schriml L, Podar M, Bork P, Weinstock G, Banfield JF, Garrity G, Hugenholtz P, Parks GH, Tyson GW, Rinke C, Dodsworth JA, Yooseph S, Sutton G, Yilmaz P, Glöckner FO, Meyer F, Gilbert J, Nelson WC, Hallam S, Jungbluth SP, Ettema T, Jetten M, Voordoeuw G, Tighe S, Konstantinidis K, Wen-Tso Liu, Baker BJ, Eren MA, Hedlund B, McMahon K, Fierer N, Eisen J, Knight R, Cochrane G, Finn R, Mizrachi I and Woyke T. (2017) Genome standards for single-cell genomes (MIxS-SCG) and genomes from metagenomes (MIxS-GFM) of bacteria and archaea. Nat Biotechnol. In review.

Steen AD, Kevorgian RT, Bird JT, Hagen SM, Mulligan KH, Dombrowski N, Baker BJ, Schmidt JM, Webber AT, Alperin MJ. (2017) Extracellular enzymes used to degrade sedimentary organic matter change with depth in anoxic estuarine sediments. Biorxiv 10.1101/080671.

Zaremba-Niedzwiedzka, K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, and Ettema TJG. (2017) ASGARD archaea illuminates the origin of eukaryotic cellular complexity. Nature In press.

Lazar CS, Baker BJ, Seitz KW, Hinrichs K-U, Teske AP (2017) Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME J. In press.

Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd K (2016) Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Frontiers in Microbiol. 7, 1221.

Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Schramm A, Stepanauskas R, Reinhardt R, Jørgensen BB, Loy A, Adrian L. (2016) Single Cell genome sequencing and targeted gene amplifications implicate members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. mBio. 7, e00266-16.

Dombrowski N, Donaho J, Teske AP, Gutierrez T, Seitz KW, Baker BJ. (2016) Hydrocarbon degradation pathways in uncultured bacteria from the Deep Water Horizon Oil Spill. Nat. Microbiol. 1, 16057.

Hug L, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle C, Butterfield CN, Hernsdorf AW, Amano Y, Suzuki Y, Dudek N, Relman DA, Thomas BC, Banfield JF (2016) A new view of The Tree of Life’s diversity. Nat Microbiol. 1, 16048.

Lazar C*, Baker BJ*, Seitz KW, Hyde AS, Dick GJ, Hinrich K-U, Teske A. (2016) Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ. Microbiol. 18, 1200-1211.   *Contributed equally

Baker BJ, Saw J, Lind A, Lazar CS, Hinrichs K-U, Teske AP, Ettema T (2016) Genomic inference of the metabolism of cosmopolitan subsurface archaea, Hadesarchaea. Nat Microbiol. 1, 16002.

Seitz KW, Lazar CS, Hinrichs K-U, Teske A, Baker BJ. (2016) Genomic reconstruction of novel, deeply-branched archaeal group capable of degradation of organic matter and sulfur cycling. ISME J. 10, 1696-1705.

Hu P, Tom LM, Singh A, Thomas BC, Baker BJ, Piceno YM, Andersen GL, Banfield JF. (2016) Genome-resolve metagenomic analysis reveals roles for candidate phyla bacteria in biogeochemical transformations in hydrocarbon reservoirs. mBio 7, e01669-15

Lazar C*, Baker BJ*, Dick GJ, Hinrich K-U, Teske A. (2016) Metabolic diversity of widespread sediment archaea. Environ. Microbiol. 18, 1200-1211.    *Contributed equally

Li M, Baker BJ, Anantharaman K, Jain S, Dick GJ. (2015) Widespread uncultured deep-sea Archaea scavenge a variety of organic compounds. Nature Comm. 6, 8933.

Baker BJ, Lazar C, Dick GJ, Teske A. (2015) Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome, 3, 14.

Baker BJ, Banfield JF. (2015) Metagenomics of acid mine drainage at Iron Mountain California: Expanding our view from individual genes and cultures to entire communities. Chapter in “Acidophiles” book.

Prior to starting at UT

Li M, Toner BM, Baker BJ, Myneni S, Dick GJ. (2014) Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Comm. 5, 3192.

Li M, Jain S, Baker BJ, Taylor C, Dick GJ. (2014) Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ. Microbiol. 16, 60-71.

Baker BJ, Dick GJ. (2013) Omic approaches in microbial ecology; charting the unknown. Microbe 8, 353-359.

Baker BJ, Taylor C, Jain S, Shiek CS, Bhasi A, Cavalcoli JD, Dick GJ. (2013) Community transcriptomic assembly reveals microbes contribute to carbon and nitrogen cycling in the deep sea. ISME J. 7, 1962-1973.

Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. (2013) The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology. 4, 1-16.

Schönknecht G, Chen W-H, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Benning C, Carr K, Wilkerson C, Rensing SA, Gagneul D, Oesterhelt C, Lercher MJ, Weber APM. (2013) Gene Transfer from Bacteria and Archaea facilitated evolution of an extremophilic eukaryote. Science. 339, 1207-1210.

Baker BJ, Lesniewski R, Dick GJ (2012) Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J. 6, 2269-2279.

Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. (2011) A unique tRNA splicing endonuclease found in ultrasmall archaeon is a chimeric protein consisting of three domains. Nucleic Acids Res. 39, 9695-9704.

Miller CS, Baker BJ, Thomas BC, Singer S, Banfield JF (2011) EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data. Genome Biology 12, R44.

Baker BJ, Comolli LR, Dick GJ, Hauser L., Land M, Hyatt, D, VerBerkmoes N, Hettich B, Banfield JF. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Natl. Acad. Sci. 107, 8806-8811.

Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes, NC, Hettich RL, Banfield, JF. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. 107, 2383-2390.

Dick GJ, Andersson, A, Baker BJ, Yelton P, Sheri SS, Thomas BC, Banfield JF. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85.

Goltsman, DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Muller R, Dick GJ, Sun C, Wheeler K, Zemla A, Baker BJ, Hauser L, Land M, Shah M, Thelen MP, Hettich RL, Banfield JF (2009) Community genomics and proteomics of chemoautotrophic, iron-oxidizing “Leptospirillum rubarum” and Leptospirillum ferrodiazotrophum populations in acid mine drainage. Appl. Environ. Microbiol. 75, 4599-4615.

Baker BJ, Tyson GW, Goosherst L, Banfield JF (2009) Insights into the diversity eukaryotes in acid mine drainage biofilm communities. Appl. Environ. Microbiol. 75, 2192-2199.

Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J. 3, 159-1671.

Baker BJ, Tyson, GW, Webb RI, Flanagan J, Hugenholtz P, Banfield JF (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314, 1933-1935.

Moser DP, Gihring TM, Brockman FJ, Fredrickson JK, Balkwill DL, Dollhopf ME, Sherwood Lollar B, Pratt LM, Boice E, Southam G, Wanger G, Baker BJ, Pfiffner SM, L-H Lin, Onstott TC. (2005) Desulfotomaculum spp. and Methanobacterium spp. a dominate 4-5 km deep fault. Appl. Environ. Microbiol. 71, 8773-8783.

Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Appl. Environ. Microbiol. 71, 6319-6324.

Ram RJ, VerBerkmoes N, Thelen MP, Tyson GW, Baker BJ, Shah M, RC Blake II, Hettich R, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308, 1915-1920.

Baker BJ, Lutz MA, Dawson SC, Bond PL, Banfield JF (2004) Metabolically active eukaryotes in extremely acidic mine drainage. Appl. Environ. Microbiol. 70, 6264-6271.

Druschel GK*, Baker BJ*, Gihring TH, Banfield JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem. Trans. 5, 13-32.                                                     *contributed equally

Moser DP, Onstott TC, Fredrickson JK, Brockman FJ, Takai K, Balkwill DL, Drake, G, Pfiffner, S, White DC, Baker BJ, Pratt LM, Fong J, Lollar BS, Slater G, Phelps TJ, Spoelstra N, DeFlaun M, Southam G, Welty AT, Hoek J (2003) Evolution of microbial community structure and geochemistry in an ultradeep South African gold mine borehole. Geomicrobiology J. 20, 517-548.

Baker BJ, Hugenholtz, P, Dawson, SC, Banfield, JF (2003) Extremely acidophilic protists host Rickettsiales-lineage endosymbionts with an intervening sequence in their 16S rRNA genes. Appl Environ. Microbiol. 69, 5512-5518.

Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. Review in FEMS Microbial Ecol. 44, 1-14.

Baker BJ, Moser DP, MacGregor BJ, Fishbain S, Wagner M, Fry N, Jackson B, Speolstra N, Loos S, Takai K, Fredrickson J, Balkwill D, Onstott TC, Wimpee CF, Stahl DA (2003)Related assemblages of sulfate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ. Microbiol. 5, 267-277.

Stahl DA, Fishbain S, Klein M, Baker BJ, Wagner M (2002) Origins and diversification of sulfate-respiring microorganisms. Antonie van Leeuwenhoek 81, 189-195.

MacGregor BJ, Van Mooy B, Baker BJ, Mellon M, Moisander PH, Pearl HW, Zehr, J, Hollander, D, Stahl DA (2001) Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Environ. Microbiol. 3, 205-209.

MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA (2001) Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ. Microbiol. 67, 3908-3922.

Sloan Foundation Fellowship in Ocean Sciences, 2016


Rackham Pre-doctoral Graduate Fellowship – 2013 competition, University of Michigan

               Funding for summer and fall 2013 through summer 2014

University of Texas College of Natural Science visualizing Science Contest 2015 – 1st place

“Using metagenomics to illuminate the biology and ecology of new branches of microbial life” Invited seminar at Cal State San Bernardino, October 2016

“Resolving the ecological roles of novel and unculutured sediment archaea.” Keynote speaker at Extremophiles 2016 conference Kyoto Japan, Sept 2016

“How genomics is enlightening microbial biodiversity and ecology of marine sediments.” Invited speaker at JAMSTIC Yokohama Japan, Sept 2016

“Using omics to expand the tree of life and resolve ecological interactions” Invited speaker at Portland State Univ, Biology Dept, May 2016 Invited speaker at Oregon Health and Science Univ, May 2016

“Using omics to expand the tree of life and resolve ecological interactions” Invited speaker at Uppsala University, Sweden in June, 2016

“Everything we know is changing: How genomics is enlightening microbial biodiversity and ecology” Biology Dept seminar series, Texas A&M Corpus Christi, May, 2016

MNS 354 - Aquatic Microbiology

MNS 191 - Scientific Commication

MNS - Genomics in Ocean Sciences

Grad Students

Kiley Seitz - PhD

Ian Rambo - PhD


Postdoctoral Researcher

Nina Dombrowski